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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere3/data/140releng-armv7-default/9476d3e04f44/logs/wfa2-lib-2.3.5.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=9476d3e04f44 Log: =>> Building biology/wfa2-lib build started at Mon May 6 11:45:51 UTC 2024 port directory: /usr/ports/biology/wfa2-lib package name: wfa2-lib-2.3.5 building for: FreeBSD 140releng-armv7-default-job-04 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 1400097 arm maintained by: j...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 396 Apr 27 01:08 /usr/ports/biology/wfa2-lib/Makefile Ports top last git commit: 9476d3e04f4 Ports top unclean checkout: no Port dir last git commit: 1de14dfc3b4 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-30-g79e3edcd Host OSVERSION: 1500018 Jail OSVERSION: 1400097 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400097 UNAME_v=FreeBSD 14.0-RELEASE-p6 1400097 UNAME_r=14.0-RELEASE-p6 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.1-30-g79e3edcd MASTERMNT=/usr/local/poudriere/data/.m/140releng-armv7-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/140releng-armv7-default/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/140releng-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work/.cache HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wfa2-lib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wfa2-lib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work/.cache HOME=/wrkdirs/usr/ports/biology/wfa2-lib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wfa2-lib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wfa2-lib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/wfa2-lib/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/wfa2-lib" EXAMPLESDIR="share/examples/wfa2-lib" DATADIR="share/wfa2-lib" WWWDIR="www/wfa2-lib" ETCDIR="etc/wfa2-lib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wfa2-lib DOCSDIR=/usr/local/share/doc/wfa2-lib EXAMPLESDIR=/usr/local/share/examples/wfa2-lib WWWDIR=/usr/local/www/wfa2-lib ETCDIR=/usr/local/etc/wfa2-lib --End SUB_LIST-- ---Begin make.conf--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wfa2-lib-2.3.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.2.pkg [140releng-armv7-default-job-04] Installing pkg-1.21.2... [140releng-armv7-default-job-04] Extracting pkg-1.21.2: .......... done ===> wfa2-lib-2.3.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of wfa2-lib-2.3.5 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by wfa2-lib-2.3.5 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by wfa2-lib-2.3.5 for building => SHA256 Checksum OK for smarco-WFA2-lib-v2.3.5_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by wfa2-lib-2.3.5 for building ===> Extracting for wfa2-lib-2.3.5 => SHA256 Checksum OK for smarco-WFA2-lib-v2.3.5_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for wfa2-lib-2.3.5 ===> Applying FreeBSD patches for wfa2-lib-2.3.5 from /usr/ports/biology/wfa2-lib/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wfa2-lib-2.3.5 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [140releng-armv7-default-job-04] Installing cmake-core-3.28.3... [140releng-armv7-default-job-04] `-- Installing expat-2.6.2... [140releng-armv7-default-job-04] `-- Extracting expat-2.6.2: .......... done [140releng-armv7-default-job-04] `-- Installing jsoncpp-1.9.5... [140releng-armv7-default-job-04] `-- Extracting jsoncpp-1.9.5: .......... done [140releng-armv7-default-job-04] `-- Installing libuv-1.48.0... [140releng-armv7-default-job-04] `-- Extracting libuv-1.48.0: .......... done [140releng-armv7-default-job-04] `-- Installing rhash-1.4.4_1... [140releng-armv7-default-job-04] | `-- Installing gettext-runtime-0.22.5... [140releng-armv7-default-job-04] | | `-- Installing indexinfo-0.3.1... [140releng-armv7-default-job-04] | | `-- Extracting indexinfo-0.3.1: .... done [140releng-armv7-default-job-04] | `-- Extracting gettext-runtime-0.22.5: .......... done [140releng-armv7-default-job-04] `-- Extracting rhash-1.4.4_1: .......... done [140releng-armv7-default-job-04] Extracting cmake-core-3.28.3: .......... done ===> wfa2-lib-2.3.5 depends on file: /usr/local/bin/cmake - found ===> Returning to build of wfa2-lib-2.3.5 ===> wfa2-lib-2.3.5 depends on executable: ninja - not found <snip> CONVERT_B_TO_MB(read_global_pos*sizeof(bt_block_t)), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/./utils/commons.h:150:33: note: expanded from macro 'CONVERT_B_TO_MB' #define CONVERT_B_TO_MB(number) ((number)/(1024*1024)) ^~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_backtrace_buffer.c:515:9: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] CONVERT_B_TO_MB(write_global_pos*sizeof(bt_block_t)), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/./utils/commons.h:150:33: note: expanded from macro 'CONVERT_B_TO_MB' #define CONVERT_B_TO_MB(number) ((number)/(1024*1024)) ^~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. [ 38% 50/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace_offload.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace_offload.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace_offload.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_backtrace_offload.c [ 39% 51/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_bialigner.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_bialigner.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_bialigner.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialigner.c [ 40% 52/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_backtrace.c [ 41% 53/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront.c [ 41% 54/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_bialign.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_bialign.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_bialign.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialign.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialign.c:676:23: warning: implicit conversion from enumeration type 'affine_matrix_type' to different enumeration type 'affine2p_matrix_type' [-Wenum-conversion] affine_matrix_M,affine_matrix_M,&breakpoint,0); ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialign.c:676:7: warning: implicit conversion from enumeration type 'affine_matrix_type' to different enumeration type 'affine2p_matrix_type' [-Wenum-conversion] affine_matrix_M,affine_matrix_M,&breakpoint,0); ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialign.c:719:25: warning: implicit conversion from enumeration type 'affine_matrix_type' to different enumeration type 'affine2p_matrix_type' [-Wenum-conversion] affine_matrix_M,affine_matrix_M, ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_bialign.c:719:9: warning: implicit conversion from enumeration type 'affine_matrix_type' to different enumeration type 'affine2p_matrix_type' [-Wenum-conversion] affine_matrix_M,affine_matrix_M, ^~~~~~~~~~~~~~~ 4 warnings generated. [ 42% 55/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_components.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_components.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_components.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_components.c [ 43% 56/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine2p.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine2p.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine2p.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_compute_affine2p.c [ 44% 57/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_compute_affine.c [ 45% 58/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_compute.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_compute.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_compute.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_compute.c [ 45% 59/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_compute_linear.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_compute_linear.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_linear.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_compute_linear.c [ 46% 60/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_debug.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_debug.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_debug.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_debug.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_debug.c:170:32: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] fprintf(stream,"\t%luMB\t",CONVERT_B_TO_MB(memory_used)); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/./utils/commons.h:150:33: note: expanded from macro 'CONVERT_B_TO_MB' #define CONVERT_B_TO_MB(number) ((number)/(1024*1024)) ^~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. [ 47% 61/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_compute_edit.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_compute_edit.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_edit.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_compute_edit.c [ 48% 62/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_extend.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_extend.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_extend.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_extend.c [ 49% 63/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_display.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_display.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_display.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_display.c [ 50% 64/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_heuristic.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_heuristic.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_heuristic.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:176:5: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] int wf_compute_distance_end2end( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:193:5: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] int wf_compute_distance_end2end_weighted( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:212:5: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] int wf_compute_distance_endsfree( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:257:6: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] void wavefront_heuristic_wfadaptive( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:257:6: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:297:6: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] void wf_heuristic_compute_sw_scores( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:329:6: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] void wavefront_heuristic_xdrop( ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_heuristic.c:400:6: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] bool wavefront_heuristic_zdrop( ^ 8 warnings generated. [ 50% 65/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_pcigar.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_pcigar.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_pcigar.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_pcigar.c [ 51% 66/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_penalties.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_penalties.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_penalties.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_penalties.c [ 52% 67/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_plot.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_plot.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_plot.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_plot.c [ 53% 68/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_slab.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_slab.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_slab.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_slab.c [ 54% 69/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_sequences.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_sequences.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_sequences.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_sequences.c [ 54% 70/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_termination.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_termination.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_termination.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_termination.c [ 55% 71/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_extend_kernels_avx.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_extend_kernels_avx.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_extend_kernels_avx.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_extend_kernels_avx.c [ 56% 72/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/wavefront/wavefront_unialign.c.o -MF CMakeFiles/wfa2.dir/wavefront/wavefront_unialign.c.o.d -o CMakeFiles/wfa2.dir/wavefront/wavefront_unialign.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_unialign.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_unialign.c:321:7: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] CONVERT_B_TO_MB(slab_size), ^~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/./utils/commons.h:150:33: note: expanded from macro 'CONVERT_B_TO_MB' #define CONVERT_B_TO_MB(number) ((number)/(1024*1024)) ^~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront/wavefront_unialign.c:322:7: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] CONVERT_B_TO_MB(bt_buffer_used), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/./utils/commons.h:150:33: note: expanded from macro 'CONVERT_B_TO_MB' #define CONVERT_B_TO_MB(number) ((number)/(1024*1024)) ^~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. 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-I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/alignment/score_matrix.c.o -MF CMakeFiles/wfa2.dir/alignment/score_matrix.c.o.d -o CMakeFiles/wfa2.dir/alignment/score_matrix.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/score_matrix.c [ 68% 87/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -MD -MT CMakeFiles/wfa2.dir/alignment/cigar.c.o -MF CMakeFiles/wfa2.dir/alignment/cigar.c.o.d -o CMakeFiles/wfa2.dir/alignment/cigar.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:50:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['M'] = SAM_CIGAR_MATCH, ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:38:26: note: expanded from macro 'SAM_CIGAR_MATCH' #define SAM_CIGAR_MATCH 0 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:51:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['I'] = SAM_CIGAR_INS, ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:39:26: note: expanded from macro 'SAM_CIGAR_INS' #define SAM_CIGAR_INS 1 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:52:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['D'] = SAM_CIGAR_DEL, ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:40:26: note: expanded from macro 'SAM_CIGAR_DEL' #define SAM_CIGAR_DEL 2 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:53:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['N'] = SAM_CIGAR_N_SKIP, ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:41:26: note: expanded from macro 'SAM_CIGAR_N_SKIP' #define SAM_CIGAR_N_SKIP 3 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:54:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['='] = SAM_CIGAR_EQ, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:42:26: note: expanded from macro 'SAM_CIGAR_EQ' #define SAM_CIGAR_EQ 7 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:55:11: warning: initializer overrides prior initialization of this subobject [-Winitializer-overrides] ['X'] = SAM_CIGAR_X, ^~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:43:26: note: expanded from macro 'SAM_CIGAR_X' #define SAM_CIGAR_X 8 ^ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:49:17: note: previous initialization is here [0 ... 255] = SAM_CIGAR_NA, ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/alignment/cigar.c:45:25: note: expanded from macro 'SAM_CIGAR_NA' #define SAM_CIGAR_NA 15 ^~ 6 warnings generated. [ 69% 88/124] : && /usr/bin/cc -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libwfa2.so.0 -o libwfa2.so.0 CMakeFiles/wfa2.dir/wavefront/wavefront_align.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_aligner.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_attributes.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace_buffer.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_backtrace_offload.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_bialign.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_bialigner.c.o CMakeFiles/wfa2.dir/wavefront/wavefront.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_components.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine2p.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_affine.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_compute.c.o CMakeFiles/wfa2.di r/wavefront/wavefront_compute_edit.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_compute_linear.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_debug.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_display.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_extend.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_heuristic.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_pcigar.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_penalties.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_plot.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_sequences.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_slab.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_unialign.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_termination.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_extend_kernels_avx.c.o CMakeFiles/wfa2.dir/wavefront/wavefront_extend_kernels.c.o CMakeFiles/wfa2.dir/system/mm_stack.c.o CMakeFiles/wfa2.dir/system/mm_allocator.c.o CMakeFiles/wfa2.dir/system/profiler_counter.c.o CMakeFiles/wfa2.dir/system/profiler_timer.c.o CMakeFiles/wfa2.di r/utils/bitmap.c.o CMakeFiles/wfa2.dir/utils/dna_text.c.o CMakeFiles/wfa2.dir/utils/sequence_buffer.c.o CMakeFiles/wfa2.dir/utils/vector.c.o CMakeFiles/wfa2.dir/utils/commons.c.o CMakeFiles/wfa2.dir/utils/heatmap.c.o CMakeFiles/wfa2.dir/alignment/affine2p_penalties.c.o CMakeFiles/wfa2.dir/alignment/affine_penalties.c.o CMakeFiles/wfa2.dir/alignment/cigar.c.o CMakeFiles/wfa2.dir/alignment/score_matrix.c.o && : [ 70% 89/124] /usr/local/bin/cmake -E cmake_symlink_library libwfa2.so.0 libwfa2.so.0 libwfa2.so && : [ 70% 90/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/system -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIE -MD -MT CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark_params.c.o -MF CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark_params.c.o.d -o CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark_params.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark_params.c [ 71% 91/124] /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/system -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIE -MD -MT CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o -MF CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o.d -o CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c FAILED: CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o /usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/system -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIE -MD -MT CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o -MF CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o.d -o CMakeFiles/align_benchmark.dir/tools/align_benchmark/align_benchmark.c.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c:32:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. [ 72% 91/124] /usr/bin/c++ -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -MD -MT CMakeFiles/wfa2cpp_static.dir/bindings/cpp/WFAligner.cpp.o -MF CMakeFiles/wfa2cpp_static.dir/bindings/cpp/WFAligner.cpp.o.d -o CMakeFiles/wfa2cpp_static.dir/bindings/cpp/WFAligner.cpp.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/bindings/cpp/WFAligner.cpp [ 73% 91/124] /usr/bin/c++ -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -Dwfa2cpp_EXPORTS -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/. -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/wavefront -I/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/utils -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -MD -MT CMakeFiles/wfa2cpp.dir/bindings/cpp/WFAligner.cpp.o -MF CMakeFiles/wfa2cpp.dir/bindings/cpp/WFAligner.cpp.o.d -o CMakeFiles/wfa2cpp.dir/bindings/cpp/WFAligner.cpp.o -c /wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/bindings/cpp/WFAligner.cpp ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/wfa2-lib
